# define paths
#base.dir <- 'https://github.com/khyde/SquidSquad.git'
base.dir <- 'C:/Users/sarah.salois/Desktop/github/khyde/SquidSquad/'
base.url <- '/'
fig.path <- 'images/'
# this is where figures will be sent
paste0(base.dir, fig.path)
# this is where markdown will point for figures
paste0(base.url, fig.path)
#knitr::include_graphics('C:/Users/sarah.salois/Documents/github/khyde/SquidSquad/images/SquidSquadV1.png')
# p5 <- ggdraw() + draw_image('C:/Users/sarah.salois/Documents/github/khyde/SquidSquad/images/SquidSquadV1.png', scale = 0.5)
# plot_grid(p5)
# <div style="display: flex;">
Weekly updates for oceanographic indicators for the Northern Shortfin Squid, Illex illecebrosus.
This page is aimed to provide near-real-time observations of relevant oceanographic conditions in the Northwest Atlantic to aid in our understanding of the patterns of availability of Illex. This page will be updated weekly and weekly observations will be retained and accessible via the table of contents in the upper left hand corner of this page. ***
Oceanographic conditions for the month of May 2022
The plots below contain mapped images of Sea Surface Temperature (SST) and Chlorophyll A (CHL) and the associated frontal dynamics for both. Additionally, you will find the Jenifer Clark charts for this week.
# This bit is an updated way to add in .png's, hopefully use to automate
# Need to decide on naming scheme and folder allocation
rundate <- "0505"
# or maybe we could pull from weekly folder 'runweek'
# here::here("images/desired.png") # gets path
# here::here("images/chl/chl_0505.png") # gets path
#knitr::include_graphics(here::here("images/chl/chl_0505.png"))
knitr::include_graphics(here::here(paste0("images/chl/chl_", rundate, ".png")))
# Another way to include images
Sea Surface Temperature
Chlorophyll
NOTES
Sea Surface Temperature
JCC May 09, 2022
JCC May 11, 2022
AG: Two WCRs in our region – both connected to the Gulf Stream with individual Squid bridges or streamers. ***
Sea Surface Temperature
Chlorophyll
JCC May 04, 2022
JCC May 06, 2022
Mean Salinity (Pioneer Array, CENTRAL)
Mean Salinity (Pioneer Array, INSHORE)
Mean Salinity (Pioneer Array, OFFSHORE)
YTD : Mean Salinity (Pioneer Array, w/2021 reference)
# Trial run :
# This works in chunk but wont knit **
jc_weekly <- list.files(here::here('images/jc_charts'),
pattern = '.png',
full.names = TRUE)
knitr::include_graphics(jc_weekly)
# This works in chunk but wont knit **
knitr::include_graphics(here::here(c("images/jc_charts/jc_0425.jpg", 'images/jc_charts/jc_0427.jpg')))
Sea Surface Temperature
Chlorophyll
JCC April 25, 2022
JCC April 27, 2022
Sea Surface Temperature
Chlorophyll
JCC April 11, 2022
JCC April 13, 2022
AG: Things are heating up with really warm GS water closing in on the shelf break near 67W!
4/11: As Adrienne predicted last week, there might be a ring forming near 67W! And look at the temperature difference between the ring water (72F) and the shelf water (48F) next to each other!
4/13: The Gulf Stream has a mind of its own! Look at the huge trough near 69-70W now!
GG: Some remarkable processes revealed in this image, including a possible squid bridge to the shelfbreak.
AM: Lots going on out there to keep track of as we inch closer to squid season. No signs of squid yet, other than some large ones in the bellies of tuna offshore
JCC April 06, 2022
JCC April 08, 2022